1) No, it should not. ISBoxer (in my experience) only displays VideoFX viewers on the active window unless you set the option to display them even when the window loses focus (can't recall the exact option name). An example of this is when using a dxNothing window to always display viewers. See this vid for an example of the VideoFX feeds on the main window disappearing when the other window(s) gets focus: http://www.youtube.com/watch?v=RFBfmk2yS2c
2) See 1.